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- PDB-8wyc: Cryo-EM structure of DSR2 (H171A)-tube-NAD+ (partial) complex -

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Basic information

Entry
Database: PDB / ID: 8wyc
TitleCryo-EM structure of DSR2 (H171A)-tube-NAD+ (partial) complex
Components
  • Bacillus phage SPR Tube protein
  • SIR2-like domain-containing protein
KeywordsANTIVIRAL PROTEIN / Phage defense proteins
Function / homologySIR2-like domain / SIR2-like domain / DHS-like NAD/FAD-binding domain superfamily / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Uncharacterized protein / SIR2-like domain-containing protein
Function and homology information
Biological speciesBacillus subtilis (bacteria)
Bacillus phage SPR (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsZhang, J.T. / Jia, N. / Liu, X.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis for phage-mediated activation and repression of bacterial DSR2 anti-phage defense system.
Authors: Jun-Tao Zhang / Xiao-Yu Liu / Zhuolin Li / Xin-Yang Wei / Xin-Yi Song / Ning Cui / Jirui Zhong / Hongchun Li / Ning Jia /
Abstract: Silent information regulator 2 (Sir2) proteins typically catalyze NAD-dependent protein deacetylation. The recently identified bacterial Sir2 domain-containing protein, defense-associated sirtuin 2 ...Silent information regulator 2 (Sir2) proteins typically catalyze NAD-dependent protein deacetylation. The recently identified bacterial Sir2 domain-containing protein, defense-associated sirtuin 2 (DSR2), recognizes the phage tail tube and depletes NAD to abort phage propagation, which is counteracted by the phage-encoded DSR anti-defense 1 (DSAD1), but their molecular mechanisms remain unclear. Here, we determine cryo-EM structures of inactive DSR2 in its apo form, DSR2-DSAD1 and DSR2-DSAD1-NAD, as well as active DSR2-tube and DSR2-tube-NAD complexes. DSR2 forms a tetramer with its C-terminal sensor domains (CTDs) in two distinct conformations: CTD or CTD. Monomeric, rather than oligomeric, tail tube proteins preferentially bind to CTD and activate Sir2 for NAD hydrolysis. DSAD1 binding to CTD allosterically inhibits tube binding and tube-mediated DSR2 activation. Our findings provide mechanistic insight into DSR2 assembly, tube-mediated DSR2 activation, and DSAD1-mediated inhibition and NAD substrate catalysis in bacterial DSR2 anti-phage defense systems.
History
DepositionOct 30, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2024Group: Data collection / Structure summary / Category: audit_author / em_author_list

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SIR2-like domain-containing protein
B: SIR2-like domain-containing protein
C: SIR2-like domain-containing protein
D: SIR2-like domain-containing protein
E: Bacillus phage SPR Tube protein
G: Bacillus phage SPR Tube protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)535,53810
Polymers532,8846
Non-polymers2,6544
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
SIR2-like domain-containing protein


Mass: 118568.727 Da / Num. of mol.: 4 / Mutation: H171A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSNT_07056 / Production host: Escherichia coli (E. coli) / References: UniProt: D4G637
#2: Protein Bacillus phage SPR Tube protein


Mass: 29304.701 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage SPR (virus) / Gene: B4122_1986 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A162TY69
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: CryoEM structure of DSR2 (H171A)-Tube NAD+ (half) complex
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Bacillus subtilis (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 85495 / Symmetry type: POINT

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